- using R version 4.5.3 Patched (2026-03-11 r89696)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-15) 15.2.0
GNU Fortran (Debian 15.2.0-15) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘lipidmapsR/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘lipidmapsR’ version ‘1.0.4’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘lipidmapsR’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] OK
- checking whether startup messages can be suppressed ... [0s/0s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [3s/5s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking examples ... [1s/20s] ERROR
Running examples in ‘lipidmapsR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compound_search
> ### Title: A function for compound search
> ### Aliases: compound_search
>
> ### ** Examples
>
>
> # Fetch compound name from LM_ID
> compound_search("lm_id", "LMFA01010001", "name")
input name
"LMFA01010001" "Palmitic acid"
>
> # Fetch all compound fields from LM_ID
> compound_search("lm_id", "LMFA01010001", "all")
input
"LMFA01010001"
regno
"101"
lm_id
"LMFA01010001"
name
"Palmitic acid"
sys_name
"hexadecanoic acid"
synonyms
"Cetylic acid; Palmitate; n-Hexadecanoic acid; C16:0; Aethalic acid "
abbrev
"FA 16:0"
core
"Fatty Acyls [FA]"
main_class
"Fatty Acids and Conjugates [FA01]"
sub_class
"Straight chain fatty acids [FA0101]"
exactmass
"256.240231"
formula
"C16H32O2"
inchi
"InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18)"
inchi_key
"IPCSVZSSVZVIGE-UHFFFAOYSA-N"
kegg_id
"C00249"
hmdb_id
"HMDB0000220"
chebi_id
"15756"
lipidbank_id
"DFA0016"
pubchem_cid
"985"
smiles
"OC(CCCCCCCCCCCCCCC)=O"
>
> # Fetch all compound fields as text from LM_ID
> compound_search("lm_id", "LMFA01010001", "all", "txt")
[1] "input\tLMFA01010001\nregno\t101\nlm_id\tLMFA01010001\nname\tPalmitic acid\nsys_name\thexadecanoic acid\nsynonyms\tCetylic acid; Palmitate; n-Hexadecanoic acid; C16:0; Aethalic acid \nabbrev\tFA 16:0\ncore\tFatty Acyls [FA]\nmain_class\tFatty Acids and Conjugates [FA01]\nsub_class\tStraight chain fatty acids [FA0101]\nexactmass\t256.240231\nformula\tC16H32O2\ninchi\tInChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18)\ninchi_key\tIPCSVZSSVZVIGE-UHFFFAOYSA-N\nkegg_id\tC00249\nhmdb_id\tHMDB0000220\nchebi_id\t15756\nlipidbank_id\tDFA0016\npubchem_cid\t985\nsmiles\tOC(CCCCCCCCCCCCCCC)=O\n\n"
>
> # Fetch compound smiles from PubChem CID
> compound_search("pubchem_cid", "985", "smiles")
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached [www.lipidmaps.org]:
Connection timed out after 10002 milliseconds
Calls: compound_search ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
- checking PDF version of manual ... [5s/8s] OK
- checking HTML version of manual ... [0s/0s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR